fmriprep

Running fmriprep
Oscar
Docker
1. Write a batch script
We keep up-to-date Singularity images for fmriprep for the community. In order to run fmriprep in Oscar, you'll need to write a batch script. We provide an example below
~/src/fmriprep_shenhav_example.sh -- Filename and not part of the script!
#!/bin/bash
#SBATCH -N 1
#SBATCH -c 8
#SBATCH --mem=24G
#SBATCH --time 18:00:00
#SBATCH -J fmriprep
#SBATCH --output fmriprep-log-%J.txt
​
#---------CONFIGURE THESE VARIABLES--------------
root_dir=/gpfs/data/bnc/mrestrep/bids-export
participant_label=tcb2002
investigator=shenhav
study_label=201226
fmriprep_version=22.0.0
#---------END OF VARIABLES------------------------
​
​
singularity run --cleanenv                                         \
  --bind ${root_dir}/${investigator}/study-${study_label}:/data    \
  --bind /gpfs/scratch/${USER}:/scratch                            \
  --bind /gpfs/data/bnc/licenses:/licenses                         \
  /gpfs/data/bnc/simgs/nipreps/fmriprep-${fmriprep_version}.sif   \
  /data/bids /data/bids/derivatives/fmriprep-${fmriprep_version}   \
  participant --participant-label ${participant_label}             \
  --fs-license-file /licenses/freesurfer-license.txt               \
  -w /scratch/fmriprep                                             \
  --omp-nthreads 16 --nthreads 16 --stop-on-first-crash
​
​
✋Understanding the batch script
The first part of the script configures the variables (e.g., number of cores, memory, etc) for your JOB
The second part invokes fmriprep singularity image. Keep in mind the following considerations:
Singularity containers run as your user, and therefore should have the same read/write permissions as your local user in the cluster
Singularity containers only share  $HOME with the Oscar file system. Therefore, any other location that we want to read and write to/from, needs to be specified using the --bind hostfolder:containerfolder input. This includes any directory in your home directory that is a symbolic link. For instance $HOME/data usually points to  /gpfs/data/<group> in that case we must bind /gpfs/data/<group>
You must specify the location inside the container of the FreeSurfer license.
✋ Troubleshooting:
fmriprep may fail for many reasons. Here are few tips:
Freesurfer is often difficult to get to completion, if it helps troubleshooting, you can turn FreeSurfer reconstruction off by adding the flag --fs-no-reconall
Familiarize yourself with the inputs and don't hesitate to ask the developers questions. Good places to look/ask for help are their GitHub issues and the Neurostars forum​
2. Run the batch script
cd ~/src
sbatch fmriprep_shenhav_example.sh
For more information about managing your job, see the Oscar documentation​
Let us know if you are interested in this documentation!
​
Getting a different version than what is installed in Oscar.
If you wish to use a version not available under /gpfs/data/bnc/simg/nipreps, you'll need to build the image. Singularity images can be large, therefore consider using a place with sufficient quota and changing the default location singularity uses to cache these files. Please see Oscar documentation.
To build the image, you can run:
version=22.0.0
singularity build fmriprep-${version}.sif docker://nipreps/fmriprep:${version}
Replace version in the command above with the desired docker tag. You can find the latest tags of fmriprep here​
 To support scientific reproducibility, it is recommended to use a specific tag e.g., 22.0.0 instead of latest 
Last modified 7mo ago